[2024-01-24 12:31:21,284] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:21,286] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:21,286] [INFO] DQC Reference Directory: /var/lib/cwl/stg1b7f3ee0-2cea-41e1-8524-1587ae420a71/dqc_reference
[2024-01-24 12:31:22,591] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:22,604] [INFO] Task started: Prodigal
[2024-01-24 12:31:22,605] [INFO] Running command: gunzip -c /var/lib/cwl/stgb355a742-24b1-455e-a28d-2ab1a7c4ff54/GCF_900129205.1_IMG-taxon_2582581272_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900129205.1_IMG-taxon_2582581272_annotated_assembly_genomic.fna/cds.fna -a GCF_900129205.1_IMG-taxon_2582581272_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:30,606] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:30,606] [INFO] Task started: HMMsearch
[2024-01-24 12:31:30,606] [INFO] Running command: hmmsearch --tblout GCF_900129205.1_IMG-taxon_2582581272_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1b7f3ee0-2cea-41e1-8524-1587ae420a71/dqc_reference/reference_markers.hmm GCF_900129205.1_IMG-taxon_2582581272_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:30,792] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:30,794] [INFO] Found 6/6 markers.
[2024-01-24 12:31:30,825] [INFO] Query marker FASTA was written to GCF_900129205.1_IMG-taxon_2582581272_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:31:30,825] [INFO] Task started: Blastn
[2024-01-24 12:31:30,825] [INFO] Running command: blastn -query GCF_900129205.1_IMG-taxon_2582581272_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b7f3ee0-2cea-41e1-8524-1587ae420a71/dqc_reference/reference_markers.fasta -out GCF_900129205.1_IMG-taxon_2582581272_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:31,711] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:31,715] [INFO] Selected 17 target genomes.
[2024-01-24 12:31:31,716] [INFO] Target genome list was writen to GCF_900129205.1_IMG-taxon_2582581272_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:31:31,725] [INFO] Task started: fastANI
[2024-01-24 12:31:31,725] [INFO] Running command: fastANI --query /var/lib/cwl/stgb355a742-24b1-455e-a28d-2ab1a7c4ff54/GCF_900129205.1_IMG-taxon_2582581272_annotated_assembly_genomic.fna.gz --refList GCF_900129205.1_IMG-taxon_2582581272_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900129205.1_IMG-taxon_2582581272_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:41,960] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:41,961] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1b7f3ee0-2cea-41e1-8524-1587ae420a71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:41,961] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1b7f3ee0-2cea-41e1-8524-1587ae420a71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:41,975] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:41,975] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:41,976] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Thermomonas hydrothermalis	strain=DSM 14834	GCA_900129205.1	213588	213588	type	True	100.0	767	770	95	conclusive
Thermomonas haemolytica	strain=DSM 13605	GCA_004346265.1	141949	141949	type	True	83.5686	582	770	95	below_threshold
Thermomonas haemolytica	strain=LMG 19653	GCA_006352395.1	141949	141949	type	True	83.5367	570	770	95	below_threshold
Thermomonas fusca	strain=DSM 15424	GCA_000423885.1	215690	215690	type	True	81.5718	527	770	95	below_threshold
Thermomonas aquatica	strain=SY21	GCA_006337105.1	2202149	2202149	type	True	80.7821	466	770	95	below_threshold
Vulcaniibacterium gelatinicum	strain=R-5-52-3	GCA_008033445.1	2598725	2598725	type	True	80.4713	411	770	95	below_threshold
Pseudoxanthomonas taiwanensis	strain=DSM 22914	GCA_010093135.1	176598	176598	type	True	80.1543	384	770	95	below_threshold
Luteimonas weifangensis	strain=WF-2	GCA_003416885.1	2303539	2303539	type	True	79.7306	426	770	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	79.4944	390	770	95	below_threshold
Lysobacter ruishenii	strain=CGMCC 1.10136	GCA_007830115.1	686800	686800	type	True	79.4568	377	770	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	79.4352	356	770	95	below_threshold
Pseudoxanthomonas jiangsuensis	strain=DSM 22398	GCA_010093185.1	619688	619688	type	True	79.4032	398	770	95	below_threshold
Pseudoxanthomonas kaohsiungensis	strain=DSM 17583	GCA_010211765.1	283923	283923	type	True	79.3126	394	770	95	below_threshold
Luteimonas padinae	strain=KCTC 52403	GCA_014652935.1	1714359	1714359	type	True	79.2331	360	770	95	below_threshold
Luteimonas viscosa	strain=XBU10	GCA_008244685.1	1132694	1132694	type	True	79.0548	385	770	95	below_threshold
Lysobacter luteus	strain=CECT 30171	GCA_907164845.1	2822368	2822368	type	True	78.9306	345	770	95	below_threshold
Lysobacter psychrotolerans	strain=ZS60	GCA_003719825.1	1327343	1327343	type	True	78.6678	344	770	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:41,978] [INFO] DFAST Taxonomy check result was written to GCF_900129205.1_IMG-taxon_2582581272_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:31:41,978] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:41,979] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:41,979] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1b7f3ee0-2cea-41e1-8524-1587ae420a71/dqc_reference/checkm_data
[2024-01-24 12:31:41,980] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:42,006] [INFO] Task started: CheckM
[2024-01-24 12:31:42,006] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900129205.1_IMG-taxon_2582581272_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900129205.1_IMG-taxon_2582581272_annotated_assembly_genomic.fna/checkm_input GCF_900129205.1_IMG-taxon_2582581272_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:32:10,968] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:10,969] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:10,991] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:10,991] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:10,992] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900129205.1_IMG-taxon_2582581272_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:32:10,992] [INFO] Task started: Blastn
[2024-01-24 12:32:10,992] [INFO] Running command: blastn -query GCF_900129205.1_IMG-taxon_2582581272_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b7f3ee0-2cea-41e1-8524-1587ae420a71/dqc_reference/reference_markers_gtdb.fasta -out GCF_900129205.1_IMG-taxon_2582581272_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:12,551] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:12,554] [INFO] Selected 13 target genomes.
[2024-01-24 12:32:12,554] [INFO] Target genome list was writen to GCF_900129205.1_IMG-taxon_2582581272_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:12,580] [INFO] Task started: fastANI
[2024-01-24 12:32:12,580] [INFO] Running command: fastANI --query /var/lib/cwl/stgb355a742-24b1-455e-a28d-2ab1a7c4ff54/GCF_900129205.1_IMG-taxon_2582581272_annotated_assembly_genomic.fna.gz --refList GCF_900129205.1_IMG-taxon_2582581272_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900129205.1_IMG-taxon_2582581272_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:20,590] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:20,600] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:20,601] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_900129205.1	s__Thermomonas hydrothermalis	100.0	767	770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004346265.1	s__Thermomonas haemolytica	83.5995	580	770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	99.99	99.99	0.99	0.99	3	-
GCA_017305095.1	s__Thermomonas sp017305095	83.233	607	770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014395425.1	s__Thermomonas brevis	82.0097	540	770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014678725.1	s__Thermomonas sp014678725	81.7768	537	770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423885.1	s__Thermomonas fusca	81.5589	528	770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	96.57	96.57	0.92	0.92	2	-
GCF_006337105.1	s__Thermomonas sp006337105	80.7947	465	770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302075.1	s__Thermomonas sp017302075	80.5685	405	770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008033445.1	s__Vulcaniibacterium_B gelatinicum	80.442	413	770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Vulcaniibacterium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830115.1	s__Lysobacter ruishenii	79.45	378	770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010211765.1	s__Pseudoxanthomonas kaohsiungensis	79.2972	396	770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652935.1	s__Luteimonas padinae	79.1937	363	770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003719825.1	s__Lysobacter psychrotolerans	78.6791	342	770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:20,602] [INFO] GTDB search result was written to GCF_900129205.1_IMG-taxon_2582581272_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:20,603] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:20,607] [INFO] DFAST_QC result json was written to GCF_900129205.1_IMG-taxon_2582581272_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:32:20,607] [INFO] DFAST_QC completed!
[2024-01-24 12:32:20,607] [INFO] Total running time: 0h0m59s